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Changeset 2:f6eb53a200df (2019-05-07)

Previous changeset 1:1b4a6ebd9898 (2018-02-12) Next changeset 3:50871000e977 (2020-07-28)

Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/autodock_vina commit ed9b6859de648aa5f7cde483732f5df20aaff90e

modified:
prepare_ligand.xml

diff -r 1b4a6ebd9898 -r f6eb53a200df prepare_ligand.xml
--- a/prepare_ligand.xml Mon Feb 12 04:23:29 2018 -0500
+++ b/prepare_ligand.xml Tue May 07 13:32:15 2019 -0400

[

b'@@ -1,5 +1,5 @@\n <tool id="prepare_ligand" name="Prepare ligand" version="0.1.0">\n- <description>Tool to prepare ligand for Autodock Vina</description>\n+ <description>for docking with Autodock Vina</description>\n <requirements>\n <requirement type="package" version="1.5.6">mgltools</requirement>\n </requirements>\n@@ -22,125 +22,138 @@\n </test>\n </tests>\n <help><![CDATA[\n-**What it does?**\n+\n+.. class:: infomark\n+\n+**What this tool does**\n \n-This tool uses the MGLTools programming packages to convert a mol2 molecule file to pdbqt molecule file, what is the Autodock Vina program uses to perform molecular docking.\n+This tool uses the MGLTools programming package to convert a mol2 molecule file to a pdbqt molecule file, which the Autodock Vina program uses to perform molecular docking. The output file has a similar format to the pdb input, with atom types modified to conform to AutoDock atom types and an extra column containing Gasteiger charges added.\n+\n+-----\n+\n+.. class:: infomark\n \n **Input**\n \n-It\'s required at least one mol2 dataset in history, what is informed in ligand field, for use the tool. The mol2 molecule file looks like the following example::\n+A mol2 file is required to use this tool.\n \n- @<TRIPOS>MOLECULE\n- NuBBE_1\n- 21 21 0 0 0\n- SMALL\n- GASTEIGER\n+* Example::\n \n- @<TRIPOS>ATOM\n- 1 O -0.9469 -0.4359 -3.2099 O.2 1 LIG1 -0.2449\n- 2 C -1.2069 0.2449 -2.2351 C.2 1 LIG1 0.3396\n- 3 O -1.9353 -0.1138 -1.1515 O.3 1 LIG1 -0.4570\n- 4 C -2.3385 -1.4828 -1.0650 C.3 1 LIG1 0.1113\n- 5 C -1.7447 -2.0319 0.2001 C.2 1 LIG1 -0.0480\n- 6 C -0.5501 -2.6439 0.3381 C.2 1 LIG1 -0.0731\n- 7 C 0.4046 -2.8855 -0.8015 C.3 1 LIG1 -0.0437\n- 8 C -0.0862 -3.1529 1.6937 C.3 1 LIG1 -0.0285\n- 9 C 0.7304 -2.1137 2.4728 C.3 1 LIG1 -0.0308\n- 10 C 1.1870 -2.6184 3.8183 C.2 1 LIG1 -0.0850\n- 11 C 2.3521 -3.2333 4.1099 C.2 1 LIG1 -0.0796\n- 12 C 3.4007 -3.6048 3.0986 C.3 1 LIG1 -0.0440\n- 13 C 2.6989 -3.6136 5.5272 C.3 1 LIG1 -0.0440\n- 14 C -0.7776 1.6572 -2.0661 C.ar 1 LIG1 0.0627\n- 15 C -0.6402 2.2240 -0.7903 C.ar 1 LIG1 -0.0026\n- 16 C -0.2486 3.5509 -0.6768 C.ar 1 LIG1 0.1590\n- 17 O -0.1045 4.1587 0.5397 O.3 1 LIG1 -0.5033\n- 18 C 0.0124 4.3080 -1.8161 C.ar 1 LIG1 0.1583\n- 19 O 0.3891 5.6141 -1.6913 O.3 1 LIG1 -0.5033\n- 20 C -0.1020 3.7535 -3.0825 C.ar 1 LIG1 -0.0158\n- 21 C -0.4936 2.4191 -3.2122 C.ar 1 LIG1 -0.0441\n- @<TRIPOS>BOND\n- 1 1 2 2\n- 2 2 3 1\n- 3 3 4 1\n- 4 4 5 1\n- 5 5 6 2\n- 6 6 7 1\n- 7 6 8 1\n- 8 8 9 1\n- 9 9 10 1\n- 10 10 11 2\n- 11 11 12 1\n- 12 11 13 1\n- 13 2 14 1\n- 14 14 15 ar\n- 15 15 16 ar\n- 16 16 17 1\n- 17 16 18 ar\n- 18 18 19 1\n- 19 18 20 ar\n- 20 20 21 ar\n- 21 14 21 ar\n+ @<TRIPOS>MOLECULE\n+ NuBBE_1\n+ 21 21 0 0 0\n+ SMALL\n+ GASTEIGER\n+ @<TRIPOS>ATOM\n+ 1 O -0.9469 -0.4359 -3.2099 O.2 1 LIG1 -0.2449\n+ 2 C -1.2069 0.2449 -2.2351 C.2 1 LIG1 '..b'0 0.099 A \n- ATOM 17 C LIG d 1 0.012 4.308 -1.816 0.00 0.00 0.098 A \n- ATOM 18 C LIG d 1 -0.102 3.753 -3.083 0.00 0.00 0.040 A \n- ATOM 19 C LIG d 1 -0.494 2.419 -3.212 0.00 0.00 0.020 A \n- BRANCH 16 20\n- ATOM 20 O LIG d 1 -0.104 4.159 0.540 0.00 0.00 -0.358 OA\n- ATOM 21 HO LIG d 1 0.164 5.067 0.617 1.00 0.00 0.217 HD\n- ENDBRANCH 16 20\n- BRANCH 17 22\n- ATOM 22 O LIG d 1 0.389 5.614 -1.691 0.00 0.00 -0.358 OA\n- ATOM 23 HO LIG d 1 0.567 6.131 -2.469 1.00 0.00 0.217 HD\n- ENDBRANCH 17 22\n- ENDBRANCH 2 14\n- TORSDOF 9\n-\n+ REMARK 9 active torsions:\n+ REMARK status: (\'A\' for Active; \'I\' for Inactive)\n+ REMARK 1 A between atoms: C_2 and O_3 \n+ REMARK 2 A between atoms: C_2 and C_14 \n+ REMARK 3 A between atoms: O_3 and C_4 \n+ REMARK 4 A between atoms: C_4 and C_5 \n+ REMARK 5 A between atoms: C_6 and C_8 \n+ REMARK 6 A between atoms: C_8 and C_9 \n+ REMARK 7 A between atoms: C_9 and C_10 \n+ REMARK 8 A between atoms: C_16 and O_17 \n+ REMARK 9 A between atoms: C_19 and O_20 \n+ ROOT\n+ ATOM 1 O LIG d 1 -0.947 -0.436 -3.210 0.00 0.00 -0.259 OA\n+ ATOM 2 C LIG d 1 -1.207 0.245 -2.235 0.00 0.00 0.293 C \n+ ENDROOT\n+ BRANCH 2 3\n+ ATOM 3 O LIG d 1 -1.935 -0.114 -1.151 0.00 0.00 -0.314 OA\n+ BRANCH 3 4\n+ ATOM 4 C LIG d 1 -2.338 -1.483 -1.065 0.00 0.00 0.206 C \n+ BRANCH 4 5\n+ ATOM 5 C LIG d 1 -1.745 -2.032 0.200 0.00 0.00 0.002 C \n+ ATOM 6 C LIG d 1 -0.550 -2.644 0.338 0.00 0.00 -0.085 C \n+ ATOM 7 C LIG d 1 0.405 -2.885 -0.801 0.00 0.00 0.043 C \n+ BRANCH 6 8\n+ ATOM 8 C LIG d 1 -0.086 -3.153 1.694 0.00 0.00 0.037 C \n+ BRANCH 8 9\n+ ATOM 9 C LIG d 1 0.730 -2.114 2.473 0.00 0.00 0.031 C \n+ BRANCH 9 10\n+ ATOM 10 C LIG d 1 1.187 -2.618 3.818 0.00 0.00 -0.024 C \n+ ATOM 11 C LIG d 1 2.352 -3.233 4.110 0.00 0.00 -0.091 C \n+ ATOM 12 C LIG d 1 3.401 -3.605 3.099 0.00 0.00 0.042 C \n+ ATOM 13 C LIG d 1 2.699 -3.614 5.527 0.00 0.00 0.042 C \n+ ENDBRANCH 9 10\n+ ENDBRANCH 8 9\n+ ENDBRANCH 6 8\n+ ENDBRANCH 4 5\n+ ENDBRANCH 3 4\n+ ENDBRANCH 2 3\n+ BRANCH 2 14\n+ ATOM 14 C LIG d 1 -0.778 1.657 -2.066 0.00 0.00 0.042 A \n+ ATOM 15 C LIG d 1 -0.640 2.224 -0.790 0.00 0.00 0.057 A \n+ ATOM 16 C LIG d 1 -0.249 3.551 -0.677 0.00 0.00 0.099 A \n+ ATOM 17 C LIG d 1 0.012 4.308 -1.816 0.00 0.00 0.098 A \n+ ATOM 18 C LIG d 1 -0.102 3.753 -3.083 0.00 0.00 0.040 A \n+ ATOM 19 C LIG d 1 -0.494 2.419 -3.212 0.00 0.00 0.020 A \n+ BRANCH 16 20\n+ ATOM 20 O LIG d 1 -0.104 4.159 0.540 0.00 0.00 -0.358 OA\n+ ATOM 21 HO LIG d 1 0.164 5.067 0.617 1.00 0.00 0.217 HD\n+ ENDBRANCH 16 20\n+ BRANCH 17 22\n+ ATOM 22 O LIG d 1 0.389 5.614 -1.691 0.00 0.00 -0.358 OA\n+ ATOM 23 HO LIG d 1 0.567 6.131 -2.469 1.00 0.00 0.217 HD\n+ ENDBRANCH 17 22\n+ ENDBRANCH 2 14\n+ TORSDOF 9\n ]]></help>\n <citations>\n <citation type="doi">10.1002/jcc.21334</citation>\n'